Need some help with themes please

hi all, im new on ere, so be gentle, iv recently been having a play with the plazmic theme creator, but i seem to be having some problems, the application text is the biggest headache, as it carrys itself into apps, so for instance even if i make a ZEN theme, and dont mess with the text at all, the text goes to black (default) which is fine on txts and stuff, but when i go into app world the texts black, rather than standard colour for app world (also does same in facebook and all other apps)
so my question is this, is there a way to lock the apps to their own text settings, so my theme doesnt mess with the apps?

and for my second problem, how do i place the file onto my website for ota downloads? i can put the .cod and .alx files in a zip then download them, but cant get the .jad file to download, it just opens up the .cod files in a text browser, is it something silly im missing??

anyways thanks in advance for the help, and heres the screen shots of my latest theme (which im lovin!)

right then iv sucesfully got it all sorted on the fonts and font colour side of things, so all is finally ready to link to, i have my own website and hosting, with FTP access direct from my laptop, but when i place a link to the .jad file, when clicked on it just opens up the page with all the .cod files listed, no download happens, is there a specific file attribute setting for thsi to work? or have i just written the link wrong? im just using the normal ahref style link